Recently, a motif shared between retroviral integrases and invertebrate transposase molecules, termed the D35E motif, has been identified. This motif is partially characterized by the first and last amino acid residues of the motif, which are an aspartate (D) and a glutamate (E), respectively. In most transposases that have been characterized, the spacing between the D and E residues is 35 amino acids, however this interval is not absolutely conserved, with spacings of 34 and 39 amino acids also having been identified. This motif is putatively involved in strand cleavage and transfer of targeted DNA, while site-specificity is conferred by a separate region of the molecule.
Progress has been made in understanding the mechanism of invertebrate transposition and retroviral integration to the point that this common D35E catalytic site has been defined in both processes, which in the case of the Tc elements of C. elegans has been shown to be a functional requirement for site-specific recombination.
Viruses such as Herpes viruses and the V(D)J recombination pathway of higher vertebrates undergo regulated site-specific recombination. Similarities between terminal and recombination signal sequences suggest that both the Herpes viruses and the immunoglobulin recombination pathway share a conserved recombination mechanism.
In the case of the Herpes viruses, the virus enters the cell in a linear form, which subsequently circularizes to enter a latent state. Following activation of the lytic cycle, the covalently closed genome then replicates via a putative "rolling circle" to yield concatameric intermediates which are then cleaved into infectious linear monomers. The molecules responsible for the Herpes virus recombination events have not been identified. There is no current description of the mechanism that Herpes viruses utilize to form the viral episome from the linear infectious form during the establishment of latency.
In vertebrates, expression of the recombinase activating gene (RAG) proteins has been identified as both necessary and sufficient to direct V(D)J recombination. In this recombination, a regulated series of site-specific recombinations occurs during development of the T and B cell lineages utilizing an interaction between "V(D)J signals" and the recombinase activating genes (RAG), RAG-1 and RAG-2. While it is known that V(D)J recombination is controlled by recombinase activating genes, the mechanism of V(D)J recombination on a molecular level is not understood.
There is a wide spectrum of need for methods and materials to control recombination events of viruses and the immune response. Interaction between recombinogenic viruses such as Herpes viruses and recombinogenic components of the immune system is in fact problematic. However, the complexity of viral life cycles and of the molecular recombination mechanisms in the immune response have hindered development of such methods and materials. Prior to the present invention, a critical component involved in recombination in non-retroviral viral life cycles and in the immune system of higher vertebrates was not appreciated. Thus, there remains a need to elucidate this component and to develop reagents and methods that would have important implications for viral infection related to pathogenesis and autoimmunity, as well as applications for gene therapy and vaccine development.